7EA8
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![BU of 7ea8 by Molmil](/molmil-images/mine/7ea8) | |
7K60
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8IEJ
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![BU of 8iej by Molmil](/molmil-images/mine/8iej) | RNF20-RNF40/hRad6A-Ub/nucleosome complex | Descriptor: | DNA (147-MER), E3 ubiquitin-protein ligase BRE1A, E3 ubiquitin-protein ligase BRE1B, ... | Authors: | Ai, H, Deng, Z, Sun, M, Du, Y, Pan, M, Liu, L. | Deposit date: | 2023-02-15 | Release date: | 2023-09-06 | Last modified: | 2023-09-20 | Method: | ELECTRON MICROSCOPY (3.12 Å) | Cite: | Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A. Mol.Cell, 83, 2023
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8JCD
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5GSE
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![BU of 5gse by Molmil](/molmil-images/mine/5gse) | Crystal structure of unusual nucleosome | Descriptor: | DNA (250-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Kato, D, Osakabe, A, Arimura, Y, Park, S.Y, Kurumizaka, H. | Deposit date: | 2016-08-16 | Release date: | 2017-05-03 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.14 Å) | Cite: | Crystal structure of the overlapping dinucleosome composed of hexasome and octasome Science, 356, 2017
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7D1Z
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![BU of 7d1z by Molmil](/molmil-images/mine/7d1z) | Cryo-EM structure of SET8-nucleosome complex | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Ho, C.-H, Takizawa, Y, Kobayashi, W, Arimura, Y, Kurumizaka, H. | Deposit date: | 2020-09-15 | Release date: | 2021-02-10 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.15 Å) | Cite: | Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase. Life Sci Alliance, 4, 2021
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5CPJ
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![BU of 5cpj by Molmil](/molmil-images/mine/5cpj) | Nucleosome containing methylated Sat2R DNA | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H. | Deposit date: | 2015-07-21 | Release date: | 2015-10-28 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biology, 5, 2015
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3L1Z
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7XX5
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![BU of 7xx5 by Molmil](/molmil-images/mine/7xx5) | Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) | Descriptor: | CALCIUM ION, DNA (169-MER), Histone H1.3, ... | Authors: | Adhireksan, Z, Qiuye, B, Lee, P.L, Sharma, D, Padavattan, S, Davey, C.A. | Deposit date: | 2022-05-28 | Release date: | 2023-05-31 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.19 Å) | Cite: | Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) To Be Published
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8JH4
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![BU of 8jh4 by Molmil](/molmil-images/mine/8jh4) | RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Akatsu, M, Fujita, R, Ogasawara, M, Ehara, H, Kujirai, T, Takizawa, Y, Sekine, S, Kurumizaka, H. | Deposit date: | 2023-05-22 | Release date: | 2023-11-29 | Last modified: | 2023-12-20 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J.Biol.Chem., 299, 2023
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3W97
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![BU of 3w97 by Molmil](/molmil-images/mine/3w97) | Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region | Descriptor: | 146-mer DNA, Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Iwasaki, W, Miya, Y, Horikoshi, N, Osakabe, A, Tachiwana, H, Shibata, T, Kagawa, W, Kurumizaka, H. | Deposit date: | 2013-04-01 | Release date: | 2013-08-28 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Contribution of histone N-terminal tails to the structure and stability of nucleosomes FEBS Open Bio, 3, 2013
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8HAG
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![BU of 8hag by Molmil](/molmil-images/mine/8hag) | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) | Descriptor: | DNA (180-mer), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | Deposit date: | 2022-10-26 | Release date: | 2023-05-17 | Last modified: | 2023-07-26 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP. Nat Commun, 14, 2023
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6LAB
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![BU of 6lab by Molmil](/molmil-images/mine/6lab) | 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 | Descriptor: | CALCIUM ION, CHLORIDE ION, DNA (169-MER), ... | Authors: | Adhireksan, Z, Sharma, D, Bao, Q, Lee, P.L, Padavattan, S, Davey, C.A. | Deposit date: | 2019-11-12 | Release date: | 2021-02-17 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Engineering nucleosomes for generating diverse chromatin assemblies. Nucleic Acids Res., 49, 2021
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8UPF
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![BU of 8upf by Molmil](/molmil-images/mine/8upf) | Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c | Descriptor: | DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. | Deposit date: | 2023-10-22 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8SMX
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![BU of 8smx by Molmil](/molmil-images/mine/8smx) | Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) | Descriptor: | DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. | Deposit date: | 2023-04-26 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8SMY
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![BU of 8smy by Molmil](/molmil-images/mine/8smy) | Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) | Descriptor: | DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. | Deposit date: | 2023-04-26 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8SMZ
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![BU of 8smz by Molmil](/molmil-images/mine/8smz) | Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) | Descriptor: | DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. | Deposit date: | 2023-04-26 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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7VCL
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3AZK
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![BU of 3azk by Molmil](/molmil-images/mine/3azk) | Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation | Descriptor: | 146-MER DNA, CHLORIDE ION, Histone H2A type 1-B/E, ... | Authors: | Iwasaki, W, Tachiwana, H, Kawaguchi, K, Shibata, T, Kagawa, W, Kurumizaka, H. | Deposit date: | 2011-05-25 | Release date: | 2011-09-21 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains Biochemistry, 50, 2011
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7ZI4
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![BU of 7zi4 by Molmil](/molmil-images/mine/7zi4) | Cryo-EM structure of the human INO80 complex bound to a WT nucleosome | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Actin-related protein 5, BERYLLIUM TRIFLUORIDE ION, ... | Authors: | Vance, N.R, Ayala, R, Willhoft, O, Tvardovskiy, A, McCormack, E.A, Bartke, T, Zhang, X, Wigley, D.B. | Deposit date: | 2022-04-07 | Release date: | 2023-04-19 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Cryo-EM structure of the human INO80 complex bound to a WT nucleosome To Be Published
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8SN0
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![BU of 8sn0 by Molmil](/molmil-images/mine/8sn0) | Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) | Descriptor: | DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. | Deposit date: | 2023-04-26 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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6T79
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![BU of 6t79 by Molmil](/molmil-images/mine/6t79) | Structure of a human nucleosome at 3.2 A resolution | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-K, ... | Authors: | Dodonova, S.O, Zhu, F, Dienemann, C, Taipale, J, Cramer, P. | Deposit date: | 2019-10-21 | Release date: | 2020-04-29 | Last modified: | 2024-05-22 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature, 580, 2020
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7XD1
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![BU of 7xd1 by Molmil](/molmil-images/mine/7xd1) | cryo-EM structure of unmodified nucleosome | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-K, ... | Authors: | Ai, H.S, Liu, A.J, Lou, Z.Y, Liu, L. | Deposit date: | 2022-03-26 | Release date: | 2022-04-20 | Last modified: | 2024-06-26 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity. Nat.Chem.Biol., 18, 2022
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7LYB
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![BU of 7lyb by Molmil](/molmil-images/mine/7lyb) | Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c | Descriptor: | BRCA1-associated RING domain protein 1, DNA (146-MER), DNA (147-MER), ... | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, D, Mer, E, Mer, G. | Deposit date: | 2021-03-06 | Release date: | 2021-07-28 | Last modified: | 2021-09-01 | Method: | ELECTRON MICROSCOPY (3.28 Å) | Cite: | Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation. Nature, 596, 2021
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4R8P
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![BU of 4r8p by Molmil](/molmil-images/mine/4r8p) | Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle | Descriptor: | DNA (147-mer), E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3, ... | Authors: | McGinty, R.K, Henrici, R.C, Tan, S. | Deposit date: | 2014-09-02 | Release date: | 2014-11-05 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (3.2846 Å) | Cite: | Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature, 514, 2014
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